## Error in library(future.apply) : 
##   there is no package called 'future.apply'

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Cut the tree at an optimal number of clusters

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  2:       1    ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  3:       1    ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  4:       1    ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  5:       1    ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  6:       1   ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  7:       1   ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  8:       1   ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  9:       1   ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10:       1   ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11:       1   ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12:       1   ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13:       1   ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14:       1   ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15:       1   ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16:       1   ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17:       1   ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18:       1   ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19:       1  NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20:       1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21:       1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22:       1   ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23:       1  NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24:       2    ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25:       2    ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26:       2    ORF8 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27:       2   ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28:       2   ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29:       2   ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30:       2   ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31:       2   ORF22 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32:       2   ORF23 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33:       2   ORF24 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34:       2   ORF25 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35:       2   ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36:       2   ORF27 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37:       2   ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38:       2   ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39:       2   ORF32 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 40:       2   ORF33 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 41:       2 ORF35.5 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 42:       2   ORF36 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 43:       2   ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 44:       2   ORF39 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 45:       2     CTO 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 46:       2   ORF40 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 47:       2   ORF42 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 48:       2   ORF43 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 49:       2   ORF44 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 50:       2   ORF46 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 51:       2   ORF49 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 52:       2   ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 53:       2   ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 54:       2   ORF58 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 55:       2   ORF59 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 56:       2   ORF62 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 57:       2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 58:       2   ORF68 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 59:       2   ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 60:       2   ORF74 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 61:       2   ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 62:       3    ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 63:       3   ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 64:       4   ORF12 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 65:       4   ORF13 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 66:       4   ORF15 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 67:       4   ORF16 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 68:       4   ORF35 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 69:       4   ORF41 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 70:       4   ORF45 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 71:       4   ORF48 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 72:       4   ORF52 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 73:       4   ORF54 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 74:       4   ORF57 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 75:       4   ORF60 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 76:       4   ORF71 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 77:       4   ORF72 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 78:       5 ORF64_1 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 79:       5   ORF75 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp         v         c      pchi
##           <num>     <num>     <num>     <num>
##  1: 0.004369945 -1.892748 0.9836849 0.7123394
##  2: 0.004369945 -1.892748 0.9836849 0.7123394
##  3: 0.004369945 -1.892748 0.9836849 0.7123394
##  4: 0.004369945 -1.892748 0.9836849 0.7123394
##  5: 0.004369945 -1.892748 0.9836849 0.7123394
##  6: 0.004369945 -1.892748 0.9836849 0.7123394
##  7: 0.004369945 -1.892748 0.9836849 0.7123394
##  8: 0.004369945 -1.892748 0.9836849 0.7123394
##  9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.005047433 -1.075907 0.6315821 0.7673805
## 40: 0.005047433 -1.075907 0.6315821 0.7673805
## 41: 0.005047433 -1.075907 0.6315821 0.7673805
## 42: 0.005047433 -1.075907 0.6315821 0.7673805
## 43: 0.005047433 -1.075907 0.6315821 0.7673805
## 44: 0.005047433 -1.075907 0.6315821 0.7673805
## 45: 0.005047433 -1.075907 0.6315821 0.7673805
## 46: 0.005047433 -1.075907 0.6315821 0.7673805
## 47: 0.005047433 -1.075907 0.6315821 0.7673805
## 48: 0.005047433 -1.075907 0.6315821 0.7673805
## 49: 0.005047433 -1.075907 0.6315821 0.7673805
## 50: 0.005047433 -1.075907 0.6315821 0.7673805
## 51: 0.005047433 -1.075907 0.6315821 0.7673805
## 52: 0.005047433 -1.075907 0.6315821 0.7673805
## 53: 0.005047433 -1.075907 0.6315821 0.7673805
## 54: 0.005047433 -1.075907 0.6315821 0.7673805
## 55: 0.005047433 -1.075907 0.6315821 0.7673805
## 56: 0.005047433 -1.075907 0.6315821 0.7673805
## 57: 0.005047433 -1.075907 0.6315821 0.7673805
## 58: 0.005047433 -1.075907 0.6315821 0.7673805
## 59: 0.005047433 -1.075907 0.6315821 0.7673805
## 60: 0.005047433 -1.075907 0.6315821 0.7673805
## 61: 0.005047433 -1.075907 0.6315821 0.7673805
## 62: 0.004877772 -1.730560 1.0893894 0.9896749
## 63: 0.004877772 -1.730560 1.0893894 0.9896749
## 64: 0.004812618 -1.784042 1.1023833 0.9849542
## 65: 0.004812618 -1.784042 1.1023833 0.9849542
## 66: 0.004812618 -1.784042 1.1023833 0.9849542
## 67: 0.004812618 -1.784042 1.1023833 0.9849542
## 68: 0.004812618 -1.784042 1.1023833 0.9849542
## 69: 0.004812618 -1.784042 1.1023833 0.9849542
## 70: 0.004812618 -1.784042 1.1023833 0.9849542
## 71: 0.004812618 -1.784042 1.1023833 0.9849542
## 72: 0.004812618 -1.784042 1.1023833 0.9849542
## 73: 0.004812618 -1.784042 1.1023833 0.9849542
## 74: 0.004812618 -1.784042 1.1023833 0.9849542
## 75: 0.004812618 -1.784042 1.1023833 0.9849542
## 76: 0.004812618 -1.784042 1.1023833 0.9849542
## 77: 0.004812618 -1.784042 1.1023833 0.9849542
## 78: 0.004577686 -0.504170 1.1633987 0.7284400
## 79: 0.004577686 -0.504170 1.1633987 0.7284400
##           se.bp         v         c      pchi

##  [1] "ORF67_1" "ORF37"   "ORF55"   "ORF32"   "ORF58"   "ORF33"   "ORF35.5"
##  [8] "ORF25"   "ORF27"   "ORF62"   "ORF45"
## [1] 11

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  2:       1    ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  3:       1    ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  4:       1    ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  5:       1    ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  6:       1   ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  7:       1   ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  8:       1   ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  9:       1   ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10:       1   ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11:       1   ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12:       1   ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13:       1   ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14:       1   ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15:       1   ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16:       1   ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17:       1   ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18:       1   ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19:       1  NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20:       1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21:       1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22:       1   ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23:       1  NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24:       2    ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25:       2    ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26:       2   ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27:       2   ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28:       2   ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29:       2   ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30:       2   ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31:       2   ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32:       2   ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33:       2   ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34:       2   ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35:       2   ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36:       2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37:       2   ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38:       2   ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39:       3    ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 40:       3   ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 41:       4    ORF8 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 42:       4   ORF22 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 43:       4   ORF23 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 44:       4   ORF24 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 45:       4   ORF25 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 46:       4   ORF27 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 47:       4   ORF32 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 48:       4   ORF33 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 49:       4 ORF35.5 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 50:       4   ORF36 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 51:       4   ORF39 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 52:       4     CTO 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 53:       4   ORF40 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 54:       4   ORF42 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 55:       4   ORF43 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 56:       4   ORF44 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 57:       4   ORF46 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 58:       4   ORF49 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 59:       4   ORF58 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 60:       4   ORF59 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 61:       4   ORF62 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 62:       4   ORF68 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 63:       4   ORF74 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 64:       5   ORF12 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 65:       5   ORF13 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 66:       5   ORF15 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 67:       5   ORF16 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 68:       5   ORF35 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 69:       5   ORF41 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 70:       5   ORF45 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 71:       5   ORF48 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 72:       5   ORF52 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 73:       5   ORF54 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 74:       5   ORF57 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 75:       5   ORF60 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 76:       5   ORF71 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 77:       5   ORF72 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 78:       6 ORF64_1 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## 79:       6   ORF75 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp         v         c      pchi
##           <num>     <num>     <num>     <num>
##  1: 0.004369945 -1.892748 0.9836849 0.7123394
##  2: 0.004369945 -1.892748 0.9836849 0.7123394
##  3: 0.004369945 -1.892748 0.9836849 0.7123394
##  4: 0.004369945 -1.892748 0.9836849 0.7123394
##  5: 0.004369945 -1.892748 0.9836849 0.7123394
##  6: 0.004369945 -1.892748 0.9836849 0.7123394
##  7: 0.004369945 -1.892748 0.9836849 0.7123394
##  8: 0.004369945 -1.892748 0.9836849 0.7123394
##  9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.004877772 -1.730560 1.0893894 0.9896749
## 40: 0.004877772 -1.730560 1.0893894 0.9896749
## 41: 0.004812618 -1.784042 1.1023833 0.9849542
## 42: 0.004812618 -1.784042 1.1023833 0.9849542
## 43: 0.004812618 -1.784042 1.1023833 0.9849542
## 44: 0.004812618 -1.784042 1.1023833 0.9849542
## 45: 0.004812618 -1.784042 1.1023833 0.9849542
## 46: 0.004812618 -1.784042 1.1023833 0.9849542
## 47: 0.004812618 -1.784042 1.1023833 0.9849542
## 48: 0.004812618 -1.784042 1.1023833 0.9849542
## 49: 0.004812618 -1.784042 1.1023833 0.9849542
## 50: 0.004812618 -1.784042 1.1023833 0.9849542
## 51: 0.004812618 -1.784042 1.1023833 0.9849542
## 52: 0.004812618 -1.784042 1.1023833 0.9849542
## 53: 0.004812618 -1.784042 1.1023833 0.9849542
## 54: 0.004812618 -1.784042 1.1023833 0.9849542
## 55: 0.004812618 -1.784042 1.1023833 0.9849542
## 56: 0.004812618 -1.784042 1.1023833 0.9849542
## 57: 0.004812618 -1.784042 1.1023833 0.9849542
## 58: 0.004812618 -1.784042 1.1023833 0.9849542
## 59: 0.004812618 -1.784042 1.1023833 0.9849542
## 60: 0.004812618 -1.784042 1.1023833 0.9849542
## 61: 0.004812618 -1.784042 1.1023833 0.9849542
## 62: 0.004812618 -1.784042 1.1023833 0.9849542
## 63: 0.004812618 -1.784042 1.1023833 0.9849542
## 64: 0.004577686 -0.504170 1.1633987 0.7284400
## 65: 0.004577686 -0.504170 1.1633987 0.7284400
## 66: 0.004577686 -0.504170 1.1633987 0.7284400
## 67: 0.004577686 -0.504170 1.1633987 0.7284400
## 68: 0.004577686 -0.504170 1.1633987 0.7284400
## 69: 0.004577686 -0.504170 1.1633987 0.7284400
## 70: 0.004577686 -0.504170 1.1633987 0.7284400
## 71: 0.004577686 -0.504170 1.1633987 0.7284400
## 72: 0.004577686 -0.504170 1.1633987 0.7284400
## 73: 0.004577686 -0.504170 1.1633987 0.7284400
## 74: 0.004577686 -0.504170 1.1633987 0.7284400
## 75: 0.004577686 -0.504170 1.1633987 0.7284400
## 76: 0.004577686 -0.504170 1.1633987 0.7284400
## 77: 0.004577686 -0.504170 1.1633987 0.7284400
## 78: 0.005235101 -1.199980 0.8922918 0.2195588
## 79: 0.005235101 -1.199980 0.8922918 0.2195588
##           se.bp         v         c      pchi

##  [1] "ORF38"   "ORF67_1" "ORF9"    "ORF11"   "ORF14"   "ORF2"    "ORF73"  
##  [8] "ORF49"   "ORF27"   "ORF32"   "ORF62"   "ORF45"
## [1] 12

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  2:       1    ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  3:       1    ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  4:       1    ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  5:       1    ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  6:       1   ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  7:       1   ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  8:       1   ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  9:       1   ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10:       1   ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11:       1   ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12:       1   ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13:       1   ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14:       1   ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15:       1   ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16:       1   ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17:       1   ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18:       1   ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19:       1  NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20:       1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21:       1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22:       1   ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23:       1  NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24:       2    ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25:       2    ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26:       2   ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27:       2   ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28:       2   ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29:       2   ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30:       2   ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31:       2   ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32:       2   ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33:       2   ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34:       2   ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35:       2   ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36:       2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37:       2   ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38:       2   ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39:       3    ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 40:       3   ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 41:       4    ORF8 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 42:       4   ORF22 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 43:       4   ORF23 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 44:       4   ORF24 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 45:       4   ORF25 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 46:       4   ORF27 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 47:       4   ORF32 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 48:       4   ORF33 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 49:       4 ORF35.5 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 50:       4   ORF36 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 51:       4   ORF39 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 52:       4     CTO 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 53:       4   ORF40 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 54:       4   ORF42 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 55:       4   ORF43 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 56:       4   ORF44 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 57:       4   ORF46 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 58:       4   ORF49 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 59:       4   ORF58 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 60:       4   ORF59 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 61:       4   ORF62 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 62:       4   ORF68 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 63:       4   ORF74 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 64:       5   ORF12 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 65:       5   ORF13 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 66:       5   ORF15 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 67:       5   ORF16 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 68:       5   ORF35 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 69:       5   ORF41 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 70:       5   ORF48 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 71:       5   ORF52 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 72:       5   ORF54 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 73:       5   ORF57 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 74:       5   ORF60 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 75:       5   ORF71 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 76:       5   ORF72 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 77:       6   ORF45 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## 78:       7 ORF64_1 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
## 79:       7   ORF75 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp         v         c      pchi
##           <num>     <num>     <num>     <num>
##  1: 0.004369945 -1.892748 0.9836849 0.7123394
##  2: 0.004369945 -1.892748 0.9836849 0.7123394
##  3: 0.004369945 -1.892748 0.9836849 0.7123394
##  4: 0.004369945 -1.892748 0.9836849 0.7123394
##  5: 0.004369945 -1.892748 0.9836849 0.7123394
##  6: 0.004369945 -1.892748 0.9836849 0.7123394
##  7: 0.004369945 -1.892748 0.9836849 0.7123394
##  8: 0.004369945 -1.892748 0.9836849 0.7123394
##  9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.004877772 -1.730560 1.0893894 0.9896749
## 40: 0.004877772 -1.730560 1.0893894 0.9896749
## 41: 0.004812618 -1.784042 1.1023833 0.9849542
## 42: 0.004812618 -1.784042 1.1023833 0.9849542
## 43: 0.004812618 -1.784042 1.1023833 0.9849542
## 44: 0.004812618 -1.784042 1.1023833 0.9849542
## 45: 0.004812618 -1.784042 1.1023833 0.9849542
## 46: 0.004812618 -1.784042 1.1023833 0.9849542
## 47: 0.004812618 -1.784042 1.1023833 0.9849542
## 48: 0.004812618 -1.784042 1.1023833 0.9849542
## 49: 0.004812618 -1.784042 1.1023833 0.9849542
## 50: 0.004812618 -1.784042 1.1023833 0.9849542
## 51: 0.004812618 -1.784042 1.1023833 0.9849542
## 52: 0.004812618 -1.784042 1.1023833 0.9849542
## 53: 0.004812618 -1.784042 1.1023833 0.9849542
## 54: 0.004812618 -1.784042 1.1023833 0.9849542
## 55: 0.004812618 -1.784042 1.1023833 0.9849542
## 56: 0.004812618 -1.784042 1.1023833 0.9849542
## 57: 0.004812618 -1.784042 1.1023833 0.9849542
## 58: 0.004812618 -1.784042 1.1023833 0.9849542
## 59: 0.004812618 -1.784042 1.1023833 0.9849542
## 60: 0.004812618 -1.784042 1.1023833 0.9849542
## 61: 0.004812618 -1.784042 1.1023833 0.9849542
## 62: 0.004812618 -1.784042 1.1023833 0.9849542
## 63: 0.004812618 -1.784042 1.1023833 0.9849542
## 64: 0.004577686 -0.504170 1.1633987 0.7284400
## 65: 0.004577686 -0.504170 1.1633987 0.7284400
## 66: 0.004577686 -0.504170 1.1633987 0.7284400
## 67: 0.004577686 -0.504170 1.1633987 0.7284400
## 68: 0.004577686 -0.504170 1.1633987 0.7284400
## 69: 0.004577686 -0.504170 1.1633987 0.7284400
## 70: 0.004577686 -0.504170 1.1633987 0.7284400
## 71: 0.004577686 -0.504170 1.1633987 0.7284400
## 72: 0.004577686 -0.504170 1.1633987 0.7284400
## 73: 0.004577686 -0.504170 1.1633987 0.7284400
## 74: 0.004577686 -0.504170 1.1633987 0.7284400
## 75: 0.004577686 -0.504170 1.1633987 0.7284400
## 76: 0.004577686 -0.504170 1.1633987 0.7284400
## 77: 0.005235101 -1.199980 0.8922918 0.2195588
## 78: 0.004959583 -1.455571 0.8971807 0.7216489
## 79: 0.004959583 -1.455571 0.8971807 0.7216489
##           se.bp         v         c      pchi

##  [1] "ORF38"   "ORF67_1" "ORF9"    "ORF11"   "ORF14"   "ORF2"    "ORF73"  
##  [8] "ORF25"   "ORF49"   "ORF27"   "ORF32"   "ORF62"   "ORF45"
## [1] 13

Selected number of clusters: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  2:       1    ORF4 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  3:       1    ORF5 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  4:       1    ORF7 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  5:       1    ORF9 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  6:       1   ORF10 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  7:       1   ORF17 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  8:       1   ORF20 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
##  9:       1   ORF21 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 10:       1   ORF30 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 11:       1   ORF31 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 12:       1   ORF34 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 13:       1   ORF38 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 14:       1   ORF50 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 15:       1   ORF53 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 16:       1   ORF56 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 17:       1   ORF61 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 18:       1   ORF63 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 19:       1  NOIR_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 20:       1 ORF65_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 21:       1 ORF67_1 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 22:       1   ORF69 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 23:       1  NOIR_2 0.9876350 0.9979890 0.8183415 0.002726923 0.0005642653
## 24:       2    ORF2 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 25:       2    ORF3 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 26:       2   ORF11 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 27:       2   ORF14 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 28:       2   ORF18 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 29:       2   ORF19 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 30:       2   ORF26 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 31:       2   ORF28 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 32:       2   ORF29 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 33:       2   ORF37 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 34:       2   ORF51 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 35:       2   ORF55 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 36:       2 ORF66_1 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 37:       2   ORF73 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 38:       2   ORF76 0.8337355 0.9561344 0.6715962 0.020368406 0.0073642528
## 39:       3    ORF6 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 40:       3   ORF70 0.9825963 0.9975984 0.7392942 0.003480760 0.0006269259
## 41:       4    ORF8 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 42:       4   ORF22 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 43:       4   ORF23 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 44:       4   ORF24 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 45:       4   ORF25 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 46:       4   ORF27 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 47:       4   ORF32 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 48:       4   ORF33 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 49:       4 ORF35.5 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 50:       4   ORF36 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 51:       4   ORF39 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 52:       4     CTO 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 53:       4   ORF40 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 54:       4   ORF42 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 55:       4   ORF43 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 56:       4   ORF44 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 57:       4   ORF46 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 58:       4   ORF49 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 59:       4   ORF58 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 60:       4   ORF59 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 61:       4   ORF62 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 62:       4   ORF68 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 63:       4   ORF74 0.9855845 0.9980518 0.7522727 0.002972510 0.0005219047
## 64:       5   ORF12 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 65:       5   ORF13 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 66:       5   ORF15 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 67:       5   ORF16 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 68:       5   ORF35 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 69:       5   ORF41 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 70:       5   ORF48 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 71:       5   ORF52 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 72:       5   ORF54 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 73:       5   ORF57 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 74:       5   ORF60 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 75:       5   ORF71 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 76:       5   ORF72 0.6100779 0.9522993 0.2548745 0.045815226 0.0090645833
## 77:       6   ORF45 0.9021746 0.9817929 0.6208402 0.013898375 0.0035533319
## 78:       7 ORF64_1 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
## 79:       7   ORF75 0.9495836 0.9906825 0.7117112 0.008344940 0.0020460314
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp         v         c      pchi
##           <num>     <num>     <num>     <num>
##  1: 0.004369945 -1.892748 0.9836849 0.7123394
##  2: 0.004369945 -1.892748 0.9836849 0.7123394
##  3: 0.004369945 -1.892748 0.9836849 0.7123394
##  4: 0.004369945 -1.892748 0.9836849 0.7123394
##  5: 0.004369945 -1.892748 0.9836849 0.7123394
##  6: 0.004369945 -1.892748 0.9836849 0.7123394
##  7: 0.004369945 -1.892748 0.9836849 0.7123394
##  8: 0.004369945 -1.892748 0.9836849 0.7123394
##  9: 0.004369945 -1.892748 0.9836849 0.7123394
## 10: 0.004369945 -1.892748 0.9836849 0.7123394
## 11: 0.004369945 -1.892748 0.9836849 0.7123394
## 12: 0.004369945 -1.892748 0.9836849 0.7123394
## 13: 0.004369945 -1.892748 0.9836849 0.7123394
## 14: 0.004369945 -1.892748 0.9836849 0.7123394
## 15: 0.004369945 -1.892748 0.9836849 0.7123394
## 16: 0.004369945 -1.892748 0.9836849 0.7123394
## 17: 0.004369945 -1.892748 0.9836849 0.7123394
## 18: 0.004369945 -1.892748 0.9836849 0.7123394
## 19: 0.004369945 -1.892748 0.9836849 0.7123394
## 20: 0.004369945 -1.892748 0.9836849 0.7123394
## 21: 0.004369945 -1.892748 0.9836849 0.7123394
## 22: 0.004369945 -1.892748 0.9836849 0.7123394
## 23: 0.004369945 -1.892748 0.9836849 0.7123394
## 24: 0.005047433 -1.075907 0.6315821 0.7673805
## 25: 0.005047433 -1.075907 0.6315821 0.7673805
## 26: 0.005047433 -1.075907 0.6315821 0.7673805
## 27: 0.005047433 -1.075907 0.6315821 0.7673805
## 28: 0.005047433 -1.075907 0.6315821 0.7673805
## 29: 0.005047433 -1.075907 0.6315821 0.7673805
## 30: 0.005047433 -1.075907 0.6315821 0.7673805
## 31: 0.005047433 -1.075907 0.6315821 0.7673805
## 32: 0.005047433 -1.075907 0.6315821 0.7673805
## 33: 0.005047433 -1.075907 0.6315821 0.7673805
## 34: 0.005047433 -1.075907 0.6315821 0.7673805
## 35: 0.005047433 -1.075907 0.6315821 0.7673805
## 36: 0.005047433 -1.075907 0.6315821 0.7673805
## 37: 0.005047433 -1.075907 0.6315821 0.7673805
## 38: 0.005047433 -1.075907 0.6315821 0.7673805
## 39: 0.004877772 -1.730560 1.0893894 0.9896749
## 40: 0.004877772 -1.730560 1.0893894 0.9896749
## 41: 0.004812618 -1.784042 1.1023833 0.9849542
## 42: 0.004812618 -1.784042 1.1023833 0.9849542
## 43: 0.004812618 -1.784042 1.1023833 0.9849542
## 44: 0.004812618 -1.784042 1.1023833 0.9849542
## 45: 0.004812618 -1.784042 1.1023833 0.9849542
## 46: 0.004812618 -1.784042 1.1023833 0.9849542
## 47: 0.004812618 -1.784042 1.1023833 0.9849542
## 48: 0.004812618 -1.784042 1.1023833 0.9849542
## 49: 0.004812618 -1.784042 1.1023833 0.9849542
## 50: 0.004812618 -1.784042 1.1023833 0.9849542
## 51: 0.004812618 -1.784042 1.1023833 0.9849542
## 52: 0.004812618 -1.784042 1.1023833 0.9849542
## 53: 0.004812618 -1.784042 1.1023833 0.9849542
## 54: 0.004812618 -1.784042 1.1023833 0.9849542
## 55: 0.004812618 -1.784042 1.1023833 0.9849542
## 56: 0.004812618 -1.784042 1.1023833 0.9849542
## 57: 0.004812618 -1.784042 1.1023833 0.9849542
## 58: 0.004812618 -1.784042 1.1023833 0.9849542
## 59: 0.004812618 -1.784042 1.1023833 0.9849542
## 60: 0.004812618 -1.784042 1.1023833 0.9849542
## 61: 0.004812618 -1.784042 1.1023833 0.9849542
## 62: 0.004812618 -1.784042 1.1023833 0.9849542
## 63: 0.004812618 -1.784042 1.1023833 0.9849542
## 64: 0.004577686 -0.504170 1.1633987 0.7284400
## 65: 0.004577686 -0.504170 1.1633987 0.7284400
## 66: 0.004577686 -0.504170 1.1633987 0.7284400
## 67: 0.004577686 -0.504170 1.1633987 0.7284400
## 68: 0.004577686 -0.504170 1.1633987 0.7284400
## 69: 0.004577686 -0.504170 1.1633987 0.7284400
## 70: 0.004577686 -0.504170 1.1633987 0.7284400
## 71: 0.004577686 -0.504170 1.1633987 0.7284400
## 72: 0.004577686 -0.504170 1.1633987 0.7284400
## 73: 0.004577686 -0.504170 1.1633987 0.7284400
## 74: 0.004577686 -0.504170 1.1633987 0.7284400
## 75: 0.004577686 -0.504170 1.1633987 0.7284400
## 76: 0.004577686 -0.504170 1.1633987 0.7284400
## 77: 0.005235101 -1.199980 0.8922918 0.2195588
## 78: 0.004959583 -1.455571 0.8971807 0.7216489
## 79: 0.004959583 -1.455571 0.8971807 0.7216489
##           se.bp         v         c      pchi

##  [1] "ORF38"   "ORF67_1" "ORF9"    "ORF11"   "ORF14"   "ORF2"    "ORF73"  
##  [8] "ORF25"   "ORF49"   "ORF27"   "ORF32"   "ORF62"   "ORF45"
## [1] 13

Remove genes from clusters ?

## The following genes were removed from their corresponding clusters 
##            as their silhouette widths were lower than 0.1 and their distance from the group centroid was higher than 0.5: 
## ORF38
## ORF67_1
## ORF9
## ORF11
## ORF14
## ORF2
## ORF73
## ORF25
## ORF49
## ORF27
## ORF32
## ORF62
## ORF45

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters